I use both Exchange and MobileMe calendars on my iphone and have never had trouble receiving alerts from either one, so my guess is that you'll have no problem. As far as I can tell, the two systems work relatively independently: any alerts from Exchange will work as usual, and any alerts from OmniFocus will be processed by the MobileMe calendars. (Note that alerts won't appear on all your Exchange devices (i.e. in Outlook) and will just be on your phone or other device connected to MobileMe.)